Directory Listing of /trilobite/notebooks/sam/robertslab.github.io/sams-notebook/posts/2023/

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2023-01-03-Daily-Bits---January-2023/2023-01-03-Daily-Bits---January-2023/ - Oct 01 2023 12:01:51 AM
2023-01-05-Monthly-Goals---January-2023/2023-01-05-Monthly-Goals---January-2023/ - Oct 01 2023 12:01:49 AM
2023-01-13-SRA-Data---Coral-SRA-BioProject-PRJNA744403-Download-and-QC/2023-01-13-SRA-Data---Coral-SRA-BioProject-PRJNA744403-Download-and-QC/ - Oct 01 2023 12:01:47 AM
2023-01-25-Genome-Indexing---M.capitata-NCBI-GCA_006542545.1-with-HiSat2-on-Mox/2023-01-25-Genome-Indexing---M.capitata-NCBI-GCA_006542545.1-with-HiSat2-on-Mox/ - Oct 01 2023 12:01:47 AM
2023-01-25-Genome-Indexing---P.verrucosa-NCBI-GCA_014529365.1-with-HiSat2-on-Mox/2023-01-25-Genome-Indexing---P.verrucosa-NCBI-GCA_014529365.1-with-HiSat2-on-Mox/ - Oct 01 2023 12:01:45 AM
2023-01-26-Data-Wrangling---P.acuta-Genome-GFF-to-GTF-Conversion-Using-gffread/2023-01-26-Data-Wrangling---P.acuta-Genome-GFF-to-GTF-Conversion-Using-gffread/ - Oct 01 2023 12:01:44 AM
2023-01-27-Data-Wrangling---M.capitata-Genome-GFF-to-GTF-Using-gffread/2023-01-27-Data-Wrangling---M.capitata-Genome-GFF-to-GTF-Using-gffread/ - Oct 01 2023 12:01:43 AM
2023-01-27-Data-Wrangling---P.verrucosa-Genome-GFF-to-GTF-Using-gffread/2023-01-27-Data-Wrangling---P.verrucosa-Genome-GFF-to-GTF-Using-gffread/ - Oct 01 2023 12:01:41 AM
2023-01-31-Genome-Indexing---M.capitata-HIv3-Assembly-with-HiSat2-on-Mox/2023-01-31-Genome-Indexing---M.capitata-HIv3-Assembly-with-HiSat2-on-Mox/ - Oct 01 2023 12:01:40 AM
2023-01-31-Genome-Indexing---P.acuta-HIv2-Assembly-with-HiSat2-on-Mox/2023-01-31-Genome-Indexing---P.acuta-HIv2-Assembly-with-HiSat2-on-Mox/ - Oct 01 2023 12:01:41 AM
2023-01-31-Genome-Indexing---P.verrucosa-v1.0-Assembly-with-HiSat2-on-Mox/2023-01-31-Genome-Indexing---P.verrucosa-v1.0-Assembly-with-HiSat2-on-Mox/ - Oct 01 2023 12:01:39 AM
2023-02-01-Daily-Bits---February-2023/2023-02-01-Daily-Bits---February-2023/ - Oct 01 2023 12:01:38 AM
2023-02-10-Data-Received---P.verrucosa-RNA-seq-and-WGBS-Full-Data-from-Danielle-Becker/2023-02-10-Data-Received---P.verrucosa-RNA-seq-and-WGBS-Full-Data-from-Danielle-Becker/ - Oct 01 2023 12:01:37 AM
2023-02-15-Data-Wrangling---Create-P.verrucosa-GCA_014529365.1-Karyotype-File/2023-02-15-Data-Wrangling---Create-P.verrucosa-GCA_014529365.1-Karyotype-File/ - Oct 01 2023 12:01:36 AM
2023-02-15-FastQ-Trimming-and-QC---P.verrucosa-RNA-seq-Data-from-Danielle-Becker-in-Hollie-Putnam-Lab-Using-fastp-FastQC-and-MultiQC-on-Mox/2023-02-15-FastQ-Trimming-and-QC---P.verrucosa-RNA-seq-Data-from-Danielle-Becker-in-Hollie-Putnam-Lab-Using-fastp-FastQC-and-MultiQC-on-Mox/ - Oct 01 2023 12:01:34 AM
2023-02-16-Transcript-Identification-and-Alignments---P.verrucosa-RNA-seq-with-Pver_genome_assembly_v1.0-Using-HiSat2-and-Stringtie-on-Mox/2023-02-16-Transcript-Identification-and-Alignments---P.verrucosa-RNA-seq-with-Pver_genome_assembly_v1.0-Using-HiSat2-and-Stringtie-on-Mox/ - Oct 01 2023 12:01:33 AM
2023-02-17-Data-Wrangling---C.goreaui-Genome-GFF-to-GTF-Using-gffread/2023-02-17-Data-Wrangling---C.goreaui-Genome-GFF-to-GTF-Using-gffread/ - Oct 01 2023 12:01:32 AM
2023-02-21-Sequencing-Read-Taxonomic-Classification---P.verrucosa-E5-RNA-seq-Using-DIAMOND-BLASTx-and-MEGAN-daa-meganizer-on-Mox/2023-02-21-Sequencing-Read-Taxonomic-Classification---P.verrucosa-E5-RNA-seq-Using-DIAMOND-BLASTx-and-MEGAN-daa-meganizer-on-Mox/ - Oct 01 2023 12:01:31 AM
2023-03-01-Data-Received---Trimmed-M.magister-RNA-seq-from-NOAA/2023-03-01-Data-Received---Trimmed-M.magister-RNA-seq-from-NOAA/ - Oct 01 2023 12:01:30 AM
2023-03-03-Daily-Bits---March-2023/2023-03-03-Daily-Bits---March-2023/ - Oct 01 2023 12:01:28 AM
2023-03-16-Sequencing-Read-Taxonomic-Classification---M.magister-RNA-seq-Using-DIAMOND-BLASTx-and-MEGAN6-daa-meganizer-on-Mox/2023-03-16-Sequencing-Read-Taxonomic-Classification---M.magister-RNA-seq-Using-DIAMOND-BLASTx-and-MEGAN6-daa-meganizer-on-Mox/ - Oct 01 2023 12:01:27 AM
2023-03-29-Data-Wrangling---Append-Gene-Ontology-Aspect-to-P.generosa-Primary-Annotation-File/2023-03-29-Data-Wrangling---Append-Gene-Ontology-Aspect-to-P.generosa-Primary-Annotation-File/ - Oct 01 2023 12:01:26 AM
2023-04-03-Daily-Bits---April-2023/2023-04-03-Daily-Bits---April-2023/ - Oct 01 2023 12:01:25 AM
2023-04-05-Data-Wrangling---CEABIGR-C.virginica-Exon-Expression-Table/2023-04-05-Data-Wrangling---CEABIGR-C.virginica-Exon-Expression-Table/ - Oct 01 2023 12:01:24 AM
2023-04-26-FastQ-Trimming-and-QC---P.generosa-RNA-seq-Data-from-20220323-on-Mox/2023-04-26-FastQ-Trimming-and-QC---P.generosa-RNA-seq-Data-from-20220323-on-Mox/ - Oct 01 2023 12:01:22 AM
2023-04-26-Transcript-Alignments---P.generosa-RNA-seq-Alignments-for-lncRNA-Identification-Using-Hisat2-StingTie-and-gffcompare-on-Mox/2023-04-26-Transcript-Alignments---P.generosa-RNA-seq-Alignments-for-lncRNA-Identification-Using-Hisat2-StingTie-and-gffcompare-on-Mox/ - Oct 01 2023 12:01:20 AM
2023-04-28-Containers---Apptainer-Explorations/2023-04-28-Containers---Apptainer-Explorations/ - Oct 01 2023 12:01:19 AM
2023-05-02-Daily-Bits---May-2023/2023-05-02-Daily-Bits---May-2023/ - Oct 01 2023 12:01:18 AM
2023-05-02-lncRNA-Identification---P.generosa-lncRNAs-using-CPC2-and-bedtools/2023-05-02-lncRNA-Identification---P.generosa-lncRNAs-using-CPC2-and-bedtools/ - Oct 01 2023 12:01:18 AM
2023-05-04-lncRNA-Expression---P.generosa-lncRNA-Expression-Using-StringTie/2023-05-04-lncRNA-Expression---P.generosa-lncRNA-Expression-Using-StringTie/ - Oct 01 2023 12:01:17 AM
2023-05-15-Data-Received---Coral-sRNA-seq-Data-from-Azenta-Project-30-852430235/2023-05-15-Data-Received---Coral-sRNA-seq-Data-from-Azenta-Project-30-852430235/ - Oct 01 2023 12:01:15 AM
2023-05-16-Data-Received---Coral-RNA-seq-Data-from-Azenta-Project-30-789513166/2023-05-16-Data-Received---Coral-RNA-seq-Data-from-Azenta-Project-30-789513166/ - Oct 01 2023 12:01:13 AM
2023-05-17-Data-Management---E5-Coral-RNA-seq-and-sRNA-seq-Reorganizing-and-Renaming/2023-05-17-Data-Management---E5-Coral-RNA-seq-and-sRNA-seq-Reorganizing-and-Renaming/ - Oct 01 2023 12:01:13 AM
2023-05-19-Data-Wrangling---P.meandrina-Genome-GFF-to-GTF-Using-gffread/2023-05-19-Data-Wrangling---P.meandrina-Genome-GFF-to-GTF-Using-gffread/ - Oct 01 2023 12:01:11 AM
2023-05-19-FastQ-QC-and-Trimming---E5-Coral-RNA-seq-Data-for-A.pulchra-P.evermanni-and-P.meandrina-Using-FastQC-fastp-and-MultiQC-on-Mox/2023-05-19-FastQ-QC-and-Trimming---E5-Coral-RNA-seq-Data-for-A.pulchra-P.evermanni-and-P.meandrina-Using-FastQC-fastp-and-MultiQC-on-Mox/ - Oct 01 2023 12:01:12 AM
2023-05-24-Trimming-and-QC---E5-Coral-sRNA-seq-Trimming-Parameter-Tests-and-Comparisons/2023-05-24-Trimming-and-QC---E5-Coral-sRNA-seq-Trimming-Parameter-Tests-and-Comparisons/ - Oct 01 2023 12:01:10 AM
2023-05-26-Repeats-Identification---P.meandrina-Using-RepeatMasker-on-Mox/2023-05-26-Repeats-Identification---P.meandrina-Using-RepeatMasker-on-Mox/ - Oct 01 2023 12:01:08 AM
2023-06-02-Daily-Bits---June-2023/2023-06-02-Daily-Bits---June-2023/ - Oct 01 2023 12:01:07 AM
2023-06-16-Transcriptome-Assembly---De-Novo-L.staminea-Trimmed-RNAseq-Using-Trinity-on-Mox/2023-06-16-Transcriptome-Assembly---De-Novo-L.staminea-Trimmed-RNAseq-Using-Trinity-on-Mox/ - Oct 01 2023 12:01:05 AM
2023-06-16-Trimming---L.staminea-RNA-seq-Using-FastQC-fastp-and-MultiQC-on-Mox/2023-06-16-Trimming---L.staminea-RNA-seq-Using-FastQC-fastp-and-MultiQC-on-Mox/ - Oct 01 2023 12:01:07 AM
2023-06-17-ORF-Identification---L.staminea-De-Novo-Transcriptome-Assembly-v1.0-Using-Transdecoder-on-Mox/2023-06-17-ORF-Identification---L.staminea-De-Novo-Transcriptome-Assembly-v1.0-Using-Transdecoder-on-Mox/ - Oct 01 2023 12:01:04 AM
2023-06-20-Trimming-and-QC---E5-Coral-sRNA-seq-Data-fro-A.pulchra-P.evermanni-and-P.meandrina-Using--FastQC-flexbar-and-MultiQC-on-Mox/2023-06-20-Trimming-and-QC---E5-Coral-sRNA-seq-Data-fro-A.pulchra-P.evermanni-and-P.meandrina-Using--FastQC-flexbar-and-MultiQC-on-Mox/ - Oct 01 2023 12:01:02 AM
2023-06-28-sRNA-seq-Alignments---E5-Coral-A.pulchra-P.meandrina-Using-ShortStack-on-Mox/2023-06-28-sRNA-seq-Alignments---E5-Coral-A.pulchra-P.meandrina-Using-ShortStack-on-Mox/ - Oct 01 2023 12:01:01 AM
2023-06-30-Data-Received---Pacific-Cod-G.macrocephalus-Sequencing-Data-from-Novogene/2023-06-30-Data-Received---Pacific-Cod-G.macrocephalus-Sequencing-Data-from-Novogene/ - Oct 01 2023 12:01:00 AM
2023-07-02-File-Conversion---M.magister-MEGANized-DAA-to-RMA6/2023-07-02-File-Conversion---M.magister-MEGANized-DAA-to-RMA6/ - Oct 01 2023 12:00:59 AM
2023-07-05-Daily-Bits---July-2023/2023-07-05-Daily-Bits---July-2023/ - Oct 01 2023 12:00:59 AM
2023-07-12-RNA-Isolation---C.gigas-Ctenidia-from-Noahs-Heat-Mechanical-Stress-Project/2023-07-12-RNA-Isolation---C.gigas-Ctenidia-from-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:57 AM
2023-07-13-qPCR---C.gigas-cDNA-Primer-Tests-for-Noahs-Heat-Mechanical-Stress-Project/2023-07-13-qPCR---C.gigas-cDNA-Primer-Tests-for-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:52 AM
2023-07-13-Reverse-Transcription---C.gigas-RNA-from-Noahs-Heat-Mechanical-Stress-Project/2023-07-13-Reverse-Transcription---C.gigas-RNA-from-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:55 AM
2023-07-13-RNA-Quantification---C.gigas-RNA-from-Noahs-Heat-Mechanical-Stress-Project/2023-07-13-RNA-Quantification---C.gigas-RNA-from-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:56 AM
2023-07-19-qPCR---C.gigas-Ctenidia-cDNA-for-Noahs-Heat-Mechanical-Stress-Project/2023-07-19-qPCR---C.gigas-Ctenidia-cDNA-for-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:49 AM
2023-07-21-qPCR---C.gigas-Ctenidia-cDNA-for-Noahs-Heat-Mechanical-Stress-Project/2023-07-21-qPCR---C.gigas-Ctenidia-cDNA-for-Noahs-Heat-Mechanical-Stress-Project/ - Oct 01 2023 12:00:48 AM
2023-07-21-Reverse-Transcription---C.gigas-PolyIC-RNA/2023-07-21-Reverse-Transcription---C.gigas-PolyIC-RNA/ - Oct 01 2023 12:00:46 AM
2023-07-21-RNA-Quantification---C.gigas-PolyIC/2023-07-21-RNA-Quantification---C.gigas-PolyIC/ - Oct 01 2023 12:00:45 AM
2023-07-26-Data-Wrangling---C.virginica-Genes-Only-FastA-from-Genes-BED-File-Using-gffread-on-Raven/2023-07-26-Data-Wrangling---C.virginica-Genes-Only-FastA-from-Genes-BED-File-Using-gffread-on-Raven/ - Oct 01 2023 12:00:43 AM
2023-07-26-qPCR---C.gigas-polyIC/2023-07-26-qPCR---C.gigas-polyIC/ - Oct 01 2023 12:00:41 AM
2023-07-26-Read-Extractions---M.magister-MEGAN-Arthropoda-and-Unassigned-Reads-to-FastA/2023-07-26-Read-Extractions---M.magister-MEGAN-Arthropoda-and-Unassigned-Reads-to-FastA/ - Oct 01 2023 12:00:44 AM
2023-07-27-DIAMOND-BLASTx---C.virginica-Genes-on-Mox/2023-07-27-DIAMOND-BLASTx---C.virginica-Genes-on-Mox/ - Oct 01 2023 12:00:40 AM
2023-07-30-Read-Extractions---M.magister-MEGAN-FastA-to-FastQ-Arthropoda-and-Unassigned-Reads/2023-07-30-Read-Extractions---M.magister-MEGAN-FastA-to-FastQ-Arthropoda-and-Unassigned-Reads/ - Oct 01 2023 12:00:39 AM
2023-07-31-sRNA-seq-Alignments---E5-Coral-P.evermanni-Using-ShortStack-on-Mox/2023-07-31-sRNA-seq-Alignments---E5-Coral-P.evermanni-Using-ShortStack-on-Mox/ - Oct 01 2023 12:00:38 AM
2023-08-01-Daily-Bits---August-2023/2023-08-01-Daily-Bits---August-2023/ - Oct 01 2023 12:00:37 AM
2023-08-16-Reverse-Transcription---C.gigas-PolyIC-Diploid-MgCl2/2023-08-16-Reverse-Transcription---C.gigas-PolyIC-Diploid-MgCl2/ - Oct 01 2023 12:00:36 AM
2023-08-16-RNA-Quantification---C.gigas-PolyIC-Diploid-MgCl2/2023-08-16-RNA-Quantification---C.gigas-PolyIC-Diploid-MgCl2/ - Oct 01 2023 12:00:36 AM
2023-08-17-qPCR---C.gigas-PolyIC-Diploid-MgCl2/2023-08-17-qPCR---C.gigas-PolyIC-Diploid-MgCl2/ - Oct 01 2023 12:00:32 AM
2023-08-21-Transcript-Identification-and-Alignments---C.virginica-RNAseq-with-NCBI-Genome-GCF_002022765.2-Using-Hisat2-and-Stringtie-on-Mox-Again/2023-08-21-Transcript-Identification-and-Alignments---C.virginica-RNAseq-with-NCBI-Genome-GCF_002022765.2-Using-Hisat2-and-Stringtie-on-Mox-Again/ - Oct 01 2023 12:00:31 AM
2023-08-22-qPCR-Analysis---C.gigas-Matt-George-Poly:IC-Diploids/2023-08-22-qPCR-Analysis---C.gigas-Matt-George-Poly:IC-Diploids/ - Oct 01 2023 12:00:30 AM
2023-08-22-qPCR-Analysis---C.gigas-Matt-George-PolyIC-Diploids/2023-08-22-qPCR-Analysis---C.gigas-Matt-George-PolyIC-Diploids/ - Dec 08 2024 12:02:47 AM
2023-11-05-Daily-Bits---November-2023/2023-11-05-Daily-Bits---November-2023/ - Nov 12 2023 12:00:43 AM
2023-11-07-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-for-DuMOAR-Project-Using-TransDecoder-on-Mox/2023-11-07-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-for-DuMOAR-Project-Using-TransDecoder-on-Mox/ - Nov 12 2023 12:42:58 AM
2023-11-09-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-for-DuMOAR-Project-Using-DIAMOND-BLASTx-on-Mox/2023-11-09-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-for-DuMOAR-Project-Using-DIAMOND-BLASTx-on-Mox/ - Nov 12 2023 12:00:41 AM
2023-11-09-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-Using-Trinotate-on-Mox/2023-11-09-Transcriptome-Annotation---M.magister-De-Novo-Transcriptome-Assembly-Using-Trinotate-on-Mox/ - Nov 12 2023 12:00:39 AM
2023-11-30-Plotting-Fun---Lab-Meeting-Task/2023-11-30-Plotting-Fun---Lab-Meeting-Task/ - Dec 03 2023 12:00:36 AM
2023-12-01-Daily-Bits---December-2023/2023-12-01-Daily-Bits---December-2023/ - Dec 03 2023 12:00:33 AM
2023-12-06-Data-Investigation---Mysterious-Case-of-Excessive-Exons-in-CEABIGR/2023-12-06-Data-Investigation---Mysterious-Case-of-Excessive-Exons-in-CEABIGR/ - Dec 10 2023 12:00:32 AM
2023-12-07-Computer-Maintenance---Replace-Failing-HDDs-in-Synology-RX1217-Expansion-Unit-on-Gannet/2023-12-07-Computer-Maintenance---Replace-Failing-HDDs-in-Synology-RX1217-Expansion-Unit-on-Gannet/ - Dec 31 2023 12:43:46 AM
2023-12-18-Samples-Submitted---Gadus-macrocephalus-liver-tissues-to-Azenta-for-RNA-seq/2023-12-18-Samples-Submitted---Gadus-macrocephalus-liver-tissues-to-Azenta-for-RNA-seq/ - Dec 24 2023 12:00:36 AM
2023-12-21-Computer-Management---Returned-Failing-HDDs-from-Gannet-Expansion-Unit/2023-12-21-Computer-Management---Returned-Failing-HDDs-from-Gannet-Expansion-Unit/ - Dec 31 2023 12:00:37 AM
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